Pope Benedict was widely regarded as having put on quite a show last week. Adopting the motto "cor ad cor loquitur" - "heart speaks unto heart" - for his visit to Britain, he seems to have heartened many Catholics. Yet his warnings about "aggressive forms of secularism" probably gave palpitations to the many atheists who saw the spectacle as a facade for promoting an anti-modern agenda and drawing a veil over the horrors of sexual abuse by the clergy.

The papal decision to beatify Cardinal Newman touched another raw nerve. Was this a deserved tribute to a great religious figure or a calculated attempt to poach other dissatisfied Anglicans into the Roman fold?

Most responses to the Pope's visit were utterly predictable. He was probably no more effective in converting atheists than his critics were in turning believers against the faith. But as long as the fault lines within religions, between religions and at the intersections of religion and science remain contested in society, the battles will continue within universities.

As everybody knows, some of the shrillest polemics have come out of the academy. Fierce attacks on God are countered by equally ferocious assaults on Richard Dawkins. Meanwhile, staff and students from many religious backgrounds and from none struggle to coexist on campus - and vice-chancellors have to find ways to build harmony. No one who feels uncomfortable, stereotyped or patronised is likely to enjoy the kind of "student experience" that all institutions now aim to provide.

Accommodating the many factions is all the more difficult because most vice-chancellors have scant regard for religion, having been educated at a time when secularism's triumph was thought to be imminent. "We are much worse at talking about religion", suggests Adam Dinham - programme director of Religious Literacy Leadership in Higher Education - in our cover feature, "because we thought we'd done away with it." Ignorance of religion and surprise that it persists are unlikely to help strategic decision-making here.

One university leader recently described his institution as embattled - "secular and therefore needing to defend that". This may be a reasonable stance, but it can be hard to carry through. There are local authorities in the US that schedule their school terms so that the holidays coincide neither with Easter nor with the Jewish spring festivals - thereby ensuring that no students get to spend time with their families on their holy days.

This may seem a rather silly compromise, but as soon as universities claim that they "won't make any allowances" for religious sensibilities in their timetables, Jews and Muslims are bound to point out that institutions tend not to hold exams or job interviews on Good Friday or Christmas Day.

When it comes to religion, universities contain a fair number of people screaming loudly that they will not talk to each other. Fortunately, there are also plenty of quiet bridge-builders: religious believers who embrace science, scientists who practise their faith in private, agnostics who prefer discussion to abuse. The ideal is not a community of angelic academics "speaking heart unto heart" but a forum where a basic respect for others' views is combined with robust but informed argument. If that isn't part of what universities should be about, it is hard to know what is.